Killing the Ghost
by William Sable
Summary: When Commander Shepard returns from the dead, many eyes take notice, including the Systems Alliance Fleet Intelligence Service. A young officer and decorated soldier is drafted for a secret mission, one that may prove to be the most difficult challenge he has ever faced: Find and Kill Commander Shepard. (ME2 Era)
1. Chapter 1: A Familiar Mission

**Chapter 1**

Clicking a pen: some people do it when they're nervous, others when they're bored. He wasn't sure which emotion made him do it, but regardless, he did.

"The Admiral will be here shortly."

The woman at the end of the table looked very much unenthused about this meeting. Her sharp Chinese features and formfitting black jumpsuit made her already intense stare all the more potent. Was he about to get a summons for a court martial or something? It's not every day that you're dragged half way across the galaxy to Alliance Naval Command for a personal meeting with an Admiral and a "representative of interested parties".

James cleared his throat, and move anxiously back and forth in his swiveling the chair. The space station's artificial gravity was noticeably lighter than most ships, and the room's dark blue, uncomfortable atmosphere made the entire thing seem very surreal. The bright white lights that extended up from the floor and arced along the curved wall and ceiling seemed to produce little light, but were all too bright to look at simultaneously.

The door hissed open. Bolting to his feet, the young officer saluted his superior and shouted "Sir!" The whole thing was meaningless in these times, but James had always had a flair for the old traditions.

"As you were Lieutenant, we have a lot to discuss." The Admiral's voice was even raspier and darker in person than James had anticipated. The Admiral sat down across the table from James. Removing his cap, he ran his hand through his hair and nodded at the mysterious woman.

Still maintaining eye contact with the woman, Admiral Hackett addressed James, "You've heard the news I presume."

"If you're referring to what I believe you're referring to, yes sir." James raised a curious eyebrow.

"We tried everything we could to contain it, but it slipped out." Hackett continued, his steady iron-like gaze shifting to James. "We also sent in a spotter, to verify. He confirmed, and then went offline."

"Sir, permission to speak freely?"

Hackett leaned back in his chair, and shot a wary glance at the woman. "Go ahead."

"With all due respect, what's this got to do with me?" he inquired, resting his elbows on the table.

"Son, we all take orders from someone." Hackett explained, furrowing his brow. "That someone has come to the conclusion that Agent Li's friends over at F.I.S. are ill-equipped to handle this sort of… operation."

The woman finally piped up, her fiery stare meeting Hackett's, "Which is untrue, but orders are orders, and this operation must go forward."

"What operation?" James questioned.

Raising a hand, Hackett continued, "I'm getting there. You've been assigned to lead a clandestine operation, top secret stuff. At this point I can't continue the briefing without you committing to the mission."

"I don't get to know what I'm committing to?"

Hackett laughed. "I don't think you *want* to know. I can say this, I know I wouldn't do it. Its risky as hell, could get you killed. A suicide mission."

"A suicide mission?" James pondered for a minute. "I'm in."

* * *

 **Author's Note:**

This is a "test" screening. If I garner good viewership for this fiction I will write and release more of it. If not, well, I have plenty of things on my schedule as is.

\- WS


	2. Chapter 2: Briefing

**Chapter 2**

The only thing worse than combat, uncertain futures, or certain death is waiting: waiting to find out which lies ahead and what to expect. It had been nearly a week since his initial briefing with Admiral Hackett, and nothing much had progressed in the terms of the mission. It wasn't until today he was summoned to a last minute meeting.

"Captain on deck!"

The uniformed man strode into the observation deck, and ordered "As you were." James thought he was a good judge of character, and his first impressions were not good. The man looked very young for a Captain. His well coifed hair was notably juxtaposed on his faded, iron-burnt and unkempt uniform. Not paying much attention to the other two people in the room, he moved swiftly towards James, with a very clear look of disappointment on his face.

"Captain Flaherty," James acknowledged, extending his hand in greeting.

"Lieutenant, let's get something straight. You may be in charge of this mission, but I am still the senior officer, and I run the show when we're aboard the ship."

James internally cringed. Why did he always get stuck with these pole-up-the-ass types? "Yes sir. Seems a bit premature, considering we haven't even been assigned a ship, wouldn't you agree?"

"That is where you are wrong, Staff Lieutenant Armstrong."

Turning to meet the source of the voice, James found himself taken by surprise. Before him stood a slender, graceful creature, with blue skin and purple lips. She was bound inside a tight grey combat suit, which hugged every curve of her body. He couldn't help but stare, remembering something about pheromones. Now he could see why the Asari were such a prolific race

His entrancement quickly came to an end as the Asari's companion, whom James hadn't notice enter the room, stepped into view. It was the woman from before.

"You all are gathered here for the same mission. We have briefed you as required prior to this meeting. I am authorized to introduce myself only as Agent Li. I will be your FIS liason for the mission." Her angry stare never seemed to cease. She had a look about her that made James instantly aggravated, which bothered him greatly. Not many people got under his skin so easily, but this was a very special group of people after all. "I will now let my associate introduce herself."

The asari stepped forward. She took a moment to gather her thoughts and observe the four humans in front of her. "Staff Lieutenant Armstrong, Captain Flaherty, Gunnery Chief Booker, and Acting Serviceman 1st Class Moldova, I greet you. I am Mirala T'vami, a member of the Special Tactics and Reconnaissance division of the Citadel fleet." Her voice was much softer than James had anticipated. "As you know, since the Battle of the Citadel, humanity has become a forefront race in galactic politics, and now has a seat on the Council. To foster warm relations amongst all Council member races, intelligence and resources must be shared in areas of common interest. As a result, I will be accompanying you on this mission as a representative of the Council's interests, though more importantly, I am an expert infiltrator and marksman."

An obvious look of distaste moved across Agent Li's face. With a somewhat hidden sigh, she robotically stated, "Mirala may be an Asari, but on this mission, she is part of the crew. Treat her as such."

Li reached her left hand to her right, and activated her omni-tool. The room suddenly came to life. A vast galaxy, with vibrant, luminous stars filled the room. James smiled. The wondrous beauty of the cosmos never left his mind, despite his heart hardening over the years. The galaxy swirled and spiraled, and suddenly exploded outward. The hologram shifted to focus on one specific system.

"You've got to be shitting me."

James turned to look at the man standing to his left. He was tall, had narrow eyes and short brown hair. His square jaw and uniform looked like a textbook example. He was a marine through and through.

"A problem, Gunnery Chief?" Mirala questioned, her brow furrowing.

"Yeah, you're damn right there's a problem," the last crewmember chimed in, "I know that system. And I know we're not welcome."

James mentally noted that this must have been Aletta Moldova. Her tied back black hair and tan skin, combined with her soft features made her look anything but an expert hacker. He had read about her in the news, about how she had hacked into the Citadel main control system undetected for two days, just to raise the gravity in her apartment.

"Ms. Moldova," Li said, stepping forward, "Need I remind you the Fleet Intelligence Service and the higher courts of the Citadel and Earth are giving you a very lenient sentence pending your cooperation on this mission. One word to my superiors and I could have this deal struck down."

"Please, Agent Li," Mirala stepped in, her voice soothing like a lullaby, "I am sure what the Acting Serviceman is referring to is the dangerous nature of the Terminus Systems. Yes, we are aware of the danger involved. But there is great danger in this entire mission."

Flaherty laughed, shaking his head, "Get in, see if Shepard is truly Shepard, kill or incapacitate, and then leave. Sounds simple to me."

"Captain, what you're failing to grasp is the environment in which we need to accomplish this," James stated, "It's like making scrambled eggs in the tundra: do-able but extremely difficult."

"That's why you're commanding," Li snapped, her ferocious gaze meeting James' cool stare, "I've been told you have a way with difficult situations."

"Why is he the one commanding anyway?" Flaherty butted in. The drawl in his voice made James want to punch him.

"Because he is the most competent, most capable and most decorated member here," Mirala answered in factual manner, sarcastically adding, "And based on records, wouldn't go anywhere in his Ceremonial Uniform if it's state was remotely like yours Captain."

"What is that supposed to mean?" Flaherty angrily shouted, advancing with a violent fire in his eyes.

"Simmer down," Li barked, "We have a job to do. If none of you have any questions or concerns, I want everyone down to Dock 12. Our ship is waiting there."

"Agent, what's her name?"


	3. Chapter 3: A Flying What?

**Chapter 3**

"What a piece of junk!"

For the first time since they had met, James finally had something to agree with Flaherty on. The ship was a little lackluster. Standing there in the hangar, staring at the dark grey and brown ship, he felt his anxiety about the coming mission beginning to increase. The thing looked liked an oversized F35 fighter jet from one of those aviation museums, but feature a paint job only a blind person could love, a frog looking throat-like bay that extended forward and topped off with additional engines on the back that looked very much out of place.

"The SSV Enigma is no junkpile, Captain Flaherty," Agent Li corrected, her voice overflowing with disdain, "It was carefully selected for maximum infiltration, and carefully modified for maximum performance."

James turned to look at Flaherty. The Captain stood for a few seconds, staring at the ship.

"It looks like a big flying turd!" he exclaimed, flailing his arms in the direction of the craft.

James shook his head and shouted, "Everyone onboard, we have a job to do."

Walking up the ramp, James adjusted his combat suit. He had a nasty habit of constantly wiping the N7 insignia on it, as if it could somehow be dulled and require shining. He already took good care of his combat dress; the armour still gleamed under the low light conditions of the sleeping beast that would be their home for the mission.

The ramp opened into a small airlock. With everyone onboard, Li retracted the ramp and pressurized the airlock. The lights flickered to life, revealing an interior very much the opposite of its exterior. The ship was the standard alliance blue steel, with trimming of white all around, and powerful lights providing a heft of brightness to the ship. Exiting the airlock, the crew entered the galley, which featured a large central table, surrounded by various food storage compartments.

"Cheer up Flaherty," Booker said, a smirk spreading across his face, "Your flying turd has leather seats."

"Stow it Chief, and that's Captain to you," Flaherty snapped back, his eyebrows angled into a frown like sharp blades.

James took stock of the ships layout from this central area. On his left, the port side of the ship extended into a hall containing doors to the armoury and the briefing room. The side opposite had a much shorter hall, with a single door on the wall that lead into the crew quarters, and at the end of the hall, one that lead into the Captain's quarters. Directly ahead, the archway turned into a long walkway, adorned with escape pods on either side. At the end of the walkway, the cockpit opened up with a wide view of the hangar outside.

"Ah! There we are!"

James cringed, as Flaherty made a b-line for the Captain's quarters. It hadn't been two hours and he hated him already.

"Make ready to undock, we make for uh…"

The room turned silent as Flaherty opened his door, and turned to look back at his comrades. A knowing look passed between them. None of them provided the answer.

After enduring the heavy silence for nearly a minute, Flaherty dismissed the situation, "Well, you know where. Chop chop!" With that, he disappeared behind the door.

Aletta made eye contact with James, and commented, "So why is he a Captain?"

Agent Li grunted, and moved toward the cockpit, stating, "His father is a very powerful man."

Wasting no time, James followed the Agent to the cockpit, and took position at the helm. The controls were very familiar, obviously modified from its original design. The engines came to life, and all gauges read green across the board. Linking his suit's microphone with the computer, James contacted Arcturus Station's control tower, and asked permission to undock and leave. After a few minutes of waiting for clearance, James finally received the go ahead. The entire time, Agent Li stood behind him, staring blankly out the window.

As the ship rose, James took a deep breath and ushered the craft forward into the dark abyss ahead. Once they were clear of the controlled zone around the Alliance Station, James opened the navicomputer and laid in a course for the nearest Mass Relay. If they wanted to get there in time, they'd have to use the Relay system to jump across the galaxy quickly.

"The Terminus Systems. No place for Alliance folk, hence the ship's design. Can I ask what design this was originally?" James said, glancing back at Li with a nervous grin, "Or is it classified?"

Li looked him dead in the eye and stated, "If I told you, I'd have to kill you."

James swallowed and returned his eyes to the screen. It read a few hours before they arrived at the Arcturus Relay. This was good, since he wanted some time to sit and think anyway.

"That was a joke, by the way."

James looked back at Li. Her face had contorted into a foreign looking, slight muscular contraction that resembled a smile.

"Ah. I thought the uptight agent thing meant no jokes, learn something every day," James joked, daring to try and pry past the stone cold façade that Li wore.

"It was Batarian in make. We've had this ship on hand since the raid at Elysium. Now, we're putting it to good use."

"Smart," James nodded, "Who would expect a ship from the one species that hates humans the most to be overflowing with humans." He chuckled, and quickly added, "That wasn't sarcasm by the way."

"I know." Li returned coldly.

James cringed, and quickly left his seat. Making his way aft, he entered the crew quarters. The room was much darker than the others, and more blue. There were 12 bunks on board, more than enough for the crew. Booker and Moldova were busy setting up their gear by their respective bunks, with a peaceful looking Mirala sitting cross-legged on the floor, meditating. James moved past them all swiftly and entered the common bathroom they shared.

The bathroom was pure white, and very sanitary. Ironic for such a skuzzy looking ship. He stared in the mirror, meeting the steely gaze emitting from his own hazel eyes. Running the water, he splashed some of it on his face. The droplets rolled off his clean shaven cheeks, though several beads became stuck in his long eyelashes. Running a gloved hand through his short, dirty blonde hair, James sighed heavily. "What have you gotten yourself into now…"

* * *

Author's Note:

Readers,

No, this is not a story about James Vega. I probably should have thought of that before naming characters, but oh well.

I thought you may be tired of hearing the same old ME characters being used over and over so I've developed new ones, with extensive backstories like they came from a Bioware game. I hope they are as interesting as time goes on.

\- WS


	4. Chapter 4: Space is Cold

**Chapter 4**

James felt his eyelids sagging as he sat at the controls. Using the propulsion of a Mass Relay shortened the time spent in interstellar travel by many tens of times, but it still took long enough to fatigue the average person. It was times like these that he felt a longing jealousy of those who had travelled in space before the discoveries of mass relays. The endless hours of sleep, time to think to oneself. Entirely the opposite of the light speed galaxy he lived in today.

"Lieutenant Armstrong."

James clicked the release on his chair and it slid back in its locked forward position. Swiveling around, he saw Mirala standing at the edge of the room. Her face appeared to glow in the pale lighting he had set for the cockpit.

"You've been up here a while. I thought I might relieve you of your flight duties for a few hours," the Asari explained, "I am trained and capable of flying this craft."

James stood up and stretched his back, "It's appreciated, thank you. I won't forget this."

Moving away from the chair he watched her take a seat. Moving toward rear of the ship, he tarried at the door a moment.

"You can drop the rank by the way. Hell, even use my first name," he stated, turning back with a grin, "You're outside the Alliance Chain of Command. And you'd be a much higher rank than me anyway."

Mirala did not move or respond for a second, staring at the controls in front of her.

"I'll consider it, Lieutenant Armstrong."

The tone in her voice was hard to read. Deciding it too hard for his tired state, James continued onward, and headed into the Crew Quarters. When he arrived, Booker was snoring loudly on his bunk, Moldova was curled up in the corner with a blanket, and Li was nowhere to be found.

James quickly stripped his combat gear off and set it inside one of the equipment lockers. Grabbing a fresh bodyglove James entered the bathroom, stripped down and hopped in the shower. The water was surprisingly warm for a deep space voyage, but he supposed the lack of fifty other crew using up all the heat had something to do with it. The water cascaded down his back, soothing his aching muscles.

Exiting the bathroom, James moved the bunk near the locker he had claimed as his own. Sitting down, the cot creaked beneath him. It wasn't exactly a motel bed, but it would do. Glancing over his shoulder, he saw that Moldova was still sitting in the corner, shivering.

James sighed, and muttered, "The things I do…"

Tearing the fire blanket off his bunk and grabbing the pillow he walked over to where the young woman was sat, ripping another bunk's blanket off as he walked. He stood nearby for a few seconds, staring at her, trying to catch her eye. She was doubled over a portable computer, shivering violently.

"Ahem."

Her head snapped up, focusing on the source of the noise.

"May I join you?" James asked, smiling nervously.

"Yeah, sure," she returned, her voice raspy and thin from fatigue.

James stepped towards her and placed the extra blanket around her shoulders, "Thought you might want this."

"Thanks." She smiled weakly, looking at James. Her gaze quickly returned back to the screen, and her fingers began typing quickly.

Lying on the ground nearby, James grunted and tried to get comfortable. Shifting into a position that was somewhat comfortable, he looked over at Moldova.

"Not one for space travel I assume?" James asked, swallowing.

"No, not really. I never even left the Presidium until…" Moldova trailed off, focusing back on her computer. The sound of the keyboard beeping at every key press was intensely quick.

James nodded, "I understand. What are you working on?"

"The ship's security network is terrible. Jimmy must have programmed it on his first day." A slight smirk spread across Aletta's face. " I'm developing an active Virtual Intelligence to detect and react to incoming threats, as well as counter attack. You won't see that on most systems, and I hope if we have to deal with any hackers, they won't expect it."

James could see the glee that had slowly poured out of her from talking about coding. Chuckling softly, he asked, "I assume your counter is a worm that will replicate obvious Trojans and viruses to cover its tracks, and then throw hydra bugs into the main system to cripple it."

Silence.

Stopping all typing, Aletta looked slowly up at James. A full on smile had worked its way across her face.

"Or something like that," James add, returning her smile.

"Not gonna lie, I may be in love with you," Aletta laughed, "Not many people care to understand the computers they use."

James felt his back tensing, and moved to another position, answering "Thank a high school career of nerdiness and the military's officer training requiring experience in every major field."

Settling in on his pillow, James felt his fatigue overruling all his senses.

"Get some sleep," he ordered, waving a tired hand in Aletta's general direction, "Your antivirus can wait a few hours. Plus, you have all the time to work on it once we're docked."

"True." Aletta shut the computer down and shoved it away. She leaned back and sighed. "I didn't catch your name. Not gonna lie, didn't catch much from the briefing."

Rolling over to face away from, the young Lieutenant felt darkness consuming his world.

"James. It's James…"


End file.
